The use of substructuring in the buckling and vibration analysis of large structures permits very substantial improvements in computational efficiency. The exact multi-level substructuring capability of the widely used computer program VICONOPT for the analysis and optimum design of prismatic plate assemblies has been extended by the inclusion of new theory, presented in this paper, which permits constraints on any of the internal or external nodes of substructures. The computational savings by using substructuring in this way are shown to be typically 50-70% compared with previous VICONOPT solutions. The theory is applicable to any method or computer code for structures whose buckling or vibration modes combine responses of different half-wavelengths, with VICONOPT being used as an example.